GreeNC

Gene information

This table contains information about coordinates, assembly and annotation regarding the lncRNA-transcribing gene. In details, it shows whether this this gene transcribes any protein-coding transcript.

Gene alias / name	Chrom.	Start	End	Assembly	Species	Details
Atauschii_AET4Gv20723000 [ AET4Gv20723000]	4D	474471251	474473912	v4	Aegilops tauschii (Ensembl Plants 51)	Coding? No

Transcript features

This table shows how a lncRNA has been classified (high/low confidence) or whether it has been classified as pre-miRNA (go to FAQ for classification criteria). Besides, it displays the lncRNA length and sequence as well as information about the ORF, the coding potential calculated by the Coding Potential Calculator (CPC), and the folding energies calculated by RNAfold.

Transcript alias / name	Confidence	Pre-miRNA	Length	Orthologous group	Sequence	Details
Atauschii_AET4Gv20723000.1 AET4Gv20723000.1	Low	No	820	OG0016401		Get ORF Coding potential... Type: coding Potential: 0.002 Folding energies... MFEI: -34.244 AMFE: -0.658 GC content %: 52.073
Atauschii_AET4Gv20723000.2 AET4Gv20723000.2	High	No	978	OG0016401		Get ORF Coding potential... Type: noncoding Potential: -0.033 Folding energies... MFEI: -32.955 AMFE: -0.623 GC content %: 52.863
Atauschii_AET4Gv20723000.3 AET4Gv20723000.3	Low	No	743	OG0016401		Get ORF Coding potential... Type: coding Potential: 0.043 Folding energies... MFEI: -35.532 AMFE: -0.663 GC content %: 53.567
Atauschii_AET4Gv20723000.4 AET4Gv20723000.4	Low	No	1456	OG0075410		Get ORF Coding potential... Type: noncoding Potential: -1.288 Folding energies... MFEI: -28.661 AMFE: -0.637 GC content %: 44.986

Matches to external databases

The lncRNAs from GreeNC have been analysed against the following databases: SwissProt, miRBase, Rfam, RepBase (RepeatMasker), NONCODE, and lncRNAdb. This table displays any association with these databases.

Transcript alias	Database	Version	Hit	Evalue
Atauschii_AET4Gv20723000.4	RepBase (RepeatMasker)	2014-01-31	LTR/Gypsy
Atauschii_AET4Gv20723000.1	RepBase (RepeatMasker)	2014-01-31	DNA

Gene models

Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).